QIIME-Galaxy

A Python application to automatically integrate QIIME on Galaxy.

Getting started

To run QIIME-Galaxy, you will first need to get QIIME and Galaxy successfully installed in your machine. Refer to their pages for installation details.

Note: QIIME-Galaxy requires Python 2.7.3 to work correctly. It has been tested with QIIME 1.7.0 and Galaxy revision 788cd3d06541+.

Installation procedure

Note: The commands in this page assume you are in your home directory. You can change the installation paths as you like, but you will need to modify the commands we provide to use the new paths.

To install QIIME-Galaxy in your system, you can follow these instructions:

1. Get the QIIME-Galaxy code by cloning the repository:

    git clone git://github.com/qiime/qiime-galaxy.git
   

Alternatively, you can download the source code in a zipped archive using this link.

2. Add the scripts folder to your path and the lib folder to your python path.

    echo "export PATH=$HOME/qiime-galaxy/scripts:$PATH" >> $HOME/.bashrc
    echo "export PYTHONPATH=$HOME/qiime-galaxy/lib:$PYTHONPATH" >> $HOME/.bashrc
    source $HOME/.bashrc
   

Usage examples

Integrate QIIME on a dedicated Galaxy instance

To integrate QIIME on a Galaxy instance that will only host the QIIME tools, run the following command. This command assumes that the Galaxy installation directory galaxy-dist and the QIIME installation directory qiime are located in your home folder. Change these paths in order to meet your system configuration.

integrate_on_galaxy.py -i $HOME/qiime/scripts -g $HOME/galaxy-dist -c $HOME/qiime-galaxy/config_file.txt

Integrate QIIME on a Galaxy instance with other tools

To integrate QIIME on a Galaxy instance that hosts other tools, run the following command. This command will allow to maintain the current Galaxy tools configuration while adding QIIME as a new available tool.

integrate_on_galaxy.py -i $HOME/qiime/scripts -g $HOME/galaxy-dist -c $HOME/qiime-galaxy/config_file.txt --update_tool_conf